Contacts of the strand formed by residues 601 - 607 (chain A) in PDB entry 4A9C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553A THR* 3.8 11.9 - - + +
554A SER 3.3 2.6 + - - -
555A PHE* 3.4 19.7 - + + +
556A GLY 2.9 24.6 + - - +
599A PHE* 4.0 2.8 - - - +
600A THR* 1.3 90.4 - - + +
602A LEU* 1.3 60.3 + - - +
603A PHE* 4.0 14.3 - - + -
695A LYS 3.8 3.8 - - - -
696A SER* 2.8 21.9 + - - +
700A THR* 3.5 36.1 - - - -
701A HIS 3.8 11.5 + - - -
702A ILE* 3.5 14.1 - - + +
727A VAL* 3.5 29.5 - - + +
728A GLY 4.3 5.7 + - - -
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLY* 3.5 15.9 - - - +
558A VAL* 4.3 19.5 - - + -
580A LEU* 5.5 0.7 - - + -
595A ILE* 3.5 30.5 - - + +
596A SER* 4.0 13.7 - - - +
599A PHE* 3.7 33.7 - - + +
600A THR 4.3 0.2 - - - -
601A HIS* 1.3 72.2 - - - +
603A PHE* 1.3 63.7 + - - +
604A TRP* 4.2 3.7 + - + -
650A PHE* 3.7 27.6 - - + -
694A TRP* 3.2 4.9 - - - +
695A LYS* 2.8 47.8 + - + +
696A SER* 5.0 0.2 + - - -
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Residues in contact with PHE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A VAL* 4.9 2.5 - - + -
428A ILE* 3.6 13.5 - - + -
555A PHE* 4.2 11.9 - + - -
556A GLY 2.7 15.2 + - - +
557A PHE* 3.4 37.3 - + + -
558A VAL* 2.8 34.0 + - - +
601A HIS* 4.0 20.6 - - + -
602A LEU* 1.3 76.3 - - - +
604A TRP* 1.3 55.8 + - - +
605A PHE* 3.8 10.1 - - + -
692A ILE* 4.9 2.2 - - + -
693A LEU 3.4 5.2 - - - +
694A TRP* 3.6 23.3 - - + -
702A ILE* 3.6 21.8 - - + -
725A PHE* 3.6 36.3 - + - -
727A VAL* 4.5 8.3 - - + -
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Residues in contact with TRP 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A VAL* 3.7 22.5 - - + +
560A CYS* 3.5 27.3 - - - -
562A LEU* 5.5 1.8 - - + +
576A TYR* 3.6 41.0 - + + -
579A ILE* 3.6 39.7 - - + -
580A LEU* 3.7 26.9 - - + -
595A ILE* 3.7 15.0 - - + -
602A LEU* 4.2 3.7 + - + -
603A PHE* 1.3 71.6 - - - +
605A PHE* 1.3 64.1 + - - +
608A LEU* 4.3 4.0 - - + -
647A PHE* 3.4 31.5 - + + -
650A PHE* 3.9 23.5 - + + -
692A ILE* 3.7 0.5 - - - -
693A LEU* 2.8 44.4 + - + +
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Residues in contact with PHE 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ILE* 3.7 20.2 - - + -
429A GLY 4.1 2.5 - - - -
430A THR* 4.1 12.6 - - - -
468A VAL* 3.6 22.7 - - + -
470A GLY* 3.7 19.1 - - - -
510A VAL* 4.0 9.0 - - + -
557A PHE* 3.9 20.6 - + + -
558A VAL 2.8 39.7 + - - +
559A ASN* 3.4 20.4 - - + -
560A CYS* 3.0 21.0 + - - -
603A PHE* 3.8 10.3 - - + -
604A TRP* 1.3 79.2 - - - +
606A GLY* 1.3 60.6 + - - +
608A LEU* 4.1 7.0 - - - -
691A ARG 3.2 16.4 - - - +
692A ILE* 3.8 16.4 - - + -
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Residues in contact with GLY 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A THR* 3.0 23.0 + - - -
472A GLN* 3.4 7.9 - - - -
559A ASN* 3.8 2.0 - - - -
560A CYS 3.3 9.0 - - - -
605A PHE* 1.3 78.4 - - - +
607A ASP* 1.3 61.0 + - - -
608A LEU* 3.3 7.3 + - - +
690A ASP* 3.4 3.7 - - - -
691A ARG 3.2 26.7 + - - +
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Residues in contact with ASP 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ASN* 2.8 24.0 + - - +
472A GLN* 3.4 20.5 - - + +
560A CYS 2.9 8.6 + - - -
561A HIS* 3.2 25.5 + - + -
562A LEU 3.0 24.1 + - - -
606A GLY* 1.3 68.8 - - - -
608A LEU* 1.4 58.4 + - - +
609A ASN* 3.2 25.2 + - - +
689A CYS* 3.4 15.1 - - - +
690A ASP* 3.7 13.2 - - - +
718A HIS* 3.5 11.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il